glam/schemas/20251121/linkml/modules/classes/BiologicalObject.yaml

id: https://nde.nl/ontology/hc/class/BiologicalObject
name: BiologicalObject
title: Biological Object Class
prefixes:
  linkml: https://w3id.org/linkml/
  hc: https://nde.nl/ontology/hc/
  schema: http://schema.org/
  crm: http://www.cidoc-crm.org/cidoc-crm/
  dcterms: http://purl.org/dc/terms/
  skos: http://www.w3.org/2004/02/skos/core#
  dwc: http://rs.tdwg.org/dwc/terms/
  gbif: http://rs.gbif.org/terms/
  aat: http://vocab.getty.edu/aat/
imports:
- linkml:types
- ../metadata
- ./TimeSpan
- ./CustodianPlace
- ../enums/PreservationMethodEnum
- ../slots/wikidata_id
- ../slots/associated_taxa
- ../slots/bold_id
- ../slots/cites_appendix
- ../slots/collection_date
- ../slots/collection_locality_text
- ../slots/collection_location
- ../slots/collector
- ../slots/common_name
- ../slots/common_name_language
- ../slots/has_or_had_custodian_type
- ../slots/date_identified
- ../slots/field_number
- ../slots/gbif_id
- ../slots/genbank_accession
- ../slots/habitat
- ../slots/higher_classification
- ../slots/identification_qualifier
- ../slots/identified_by
- ../slots/is_type_specimen
- ../slots/iucn_status
- ../slots/legal_provenance_note
- ../slots/life_stage
- ../slots/part_type
- ../slots/preparation_date
- ../slots/prepared_by
- ../slots/preservation_method
- ../slots/preservative_detail
- ../slots/sex
- ../slots/specificity_annotation
- ../slots/specimen_count
- ../slots/specimen_type
- ../slots/taxon_name
- ../slots/taxon_remark
- ../slots/taxonomic_authority
- ../slots/taxonomic_rank
- ../slots/template_specificity
- ../slots/type_status
- ./SpecificityAnnotation
- ./TemplateSpecificityScores
default_prefix: hc
classes:
  BiologicalObject:
    class_uri: crm:E20_Biological_Object
    description: "A biological specimen or natural history object held in a heritage\
      \ collection.\n\nModels organisms, parts of organisms, or biological products\
      \ preserved for\nscientific study, education, or display.\n\n**CIDOC-CRM Alignment**:\n\
      \nE20_Biological_Object - \"Physical objects that have been produced by \nbiological\
      \ processes and include organisms, parts of organisms, and \nbiological products.\"\
      \n\n**Key Distinction from ExhibitedObject**:\n\n| Concept | Class | Example\
      \ |\n|---------|-------|---------|\n| General museum object | ExhibitedObject\
      \ | \"Girl with a Pearl Earring\" |\n| **Biological specimen** | **BiologicalObject**\
      \ | **Dodo skeleton** |\n| Archaeological find | ExhibitedObject | Roman pottery\
      \ |\n\n**When to Use BiologicalObject**:\n\nUse for specimens that are primarily\
      \ biological in nature:\n- Taxidermy mounts (mammals, birds, fish)\n- Study\
      \ skins and skeletal material\n- Herbarium specimens (pressed plants)\n- Wet\
      \ specimens (fluid-preserved animals)\n- Fossils of organisms\n- Entomological\
      \ collections (pinned insects)\n- Paleontological specimens\n- Living collection\
      \ records (botanical gardens, zoos)\n\n**Darwin Core Integration**:\n\nBiologicalObject\
      \ aligns with Darwin Core (TDWG) occurrence/specimen standards:\n- `taxon_name`\
      \ → dwc:scientificName\n- `collection_date` → dwc:eventDate\n- `collector` →\
      \ dwc:recordedBy\n- `preservation_method` → dwc:preparations\n- `gbif_id` →\
      \ dwc:occurrenceID (GBIF)\n\n**Taxonomic Data Model**:\n\n```\nBiologicalObject\n\
      \    │\n    ├── taxon_name (scientific name: \"Raphus cucullatus\")\n    │ \
      \      │\n    │       ├── common_name (\"Dodo\")\n    │       ├── taxonomic_rank\
      \ (SPECIES)\n    │       ├── taxonomic_authority (\"Linnaeus, 1758\")\n    │\
      \       └── higher_classification (Aves → Columbiformes → Columbidae)\n    │\n\
      \    ├── specimen_data\n    │       │\n    │       ├── specimen_type (HOLOTYPE,\
      \ PARATYPE, etc.)\n    │       ├── is_type_specimen (boolean)\n    │       ├──\
      \ sex (MALE, FEMALE, UNKNOWN)\n    │       ├── life_stage (ADULT, JUVENILE,\
      \ LARVA, etc.)\n    │       └── part_type (SKELETON, SKIN, SHELL, etc.)\n  \
      \  │\n    ├── preservation\n    │       │\n    │       ├── preservation_method\
      \ (PreservationMethodEnum)\n    │       └── preservative_details (specific chemicals,\
      \ methods)\n    │\n    └── collection_event\n            │\n            ├──\
      \ collection_date (when collected)\n            ├── collection_location (where\
      \ collected)\n            ├── collector (who collected)\n            └── field_number\
      \ (collector's field ID)\n```\n\n**Conservation Status Integration**:\n\nFor\
      \ specimens of conservation-sensitive species, BiologicalObject supports:\n\
      - IUCN Red List status tracking\n- CITES appendix listing\n- Provenance documentation\
      \ for legal compliance\n\n**Example**:\n\nOxford Dodo specimen at Oxford University\
      \ Museum of Natural History:\n- taxon_name: \"Raphus cucullatus\"\n- common_name:\
      \ \"Dodo\"\n- specimen_type: Historical specimen\n- preservation_method: SKELETON\
      \ (partial)\n- significance: Last reliably dated dodo remains\n"
    exact_mappings:
    - crm:E20_Biological_Object
    close_mappings:
    - dwc:Occurrence
    - dwc:Organism
    - schema:Taxon
    related_mappings:
    - crm:E19_Physical_Object
    - crm:E22_Human-Made_Object
    - gbif:Specimen
    is_a: ExhibitedObject
    slots:
    - associated_taxa
    - bold_id
    - cites_appendix
    - collection_date
    - collection_locality_text
    - collection_location
    - collector
    - common_name
    - common_name_language
    - has_or_had_custodian_type
    - date_identified
    - field_number
    - gbif_id
    - genbank_accession
    - habitat
    - higher_classification
    - identification_qualifier
    - identified_by
    - is_type_specimen
    - iucn_status
    - legal_provenance_note
    - life_stage
    - part_type
    - preparation_date
    - prepared_by
    - preservation_method
    - preservative_detail
    - sex
    - specificity_annotation
    - specimen_count
    - specimen_type
    - taxon_name
    - taxon_remark
    - taxonomic_authority
    - taxonomic_rank
    - template_specificity
    - type_status
    slot_usage:
      taxon_name:
        required: true
        range: string
        slot_uri: dwc:scientificName
        description: |
          Scientific name (Linnean binomial or trinomial).
          Include author and year for formal nomenclature.

          **Format**: "Genus species (Author, Year)"

          **Examples**:
          - "Raphus cucullatus (Linnaeus, 1758)"
          - "Tyrannosaurus rex Osborn, 1905"
          - "Quercus robur L."          
        examples:
        - value: Raphus cucullatus (Linnaeus, 1758)
          description: Dodo with nomenclatural authority
        - value: Panthera leo
          description: Lion (authority omitted)
      common_name:
        required: false
        range: string
        multivalued: true
        slot_uri: dwc:vernacularName
        description: |
          Common/vernacular name(s) in one or more languages.
          Use common_name_language to specify language.          
        examples:
        - value: Dodo
        - value: Lion
        - value: Coast Redwood
      common_name_language:
        required: false
        range: string
        multivalued: true
        slot_uri: dcterms:language
        description: |
          Language code(s) for common names (ISO 639-1 or 639-3).
          Corresponds to common_name list by position.          
        examples:
        - value: en
        - value: nl
      taxonomic_rank:
        required: false
        range: string
        slot_uri: dwc:taxonRank
        description: "Taxonomic rank of the identification.\n\n**Values**: KINGDOM,\
          \ PHYLUM, CLASS, ORDER, FAMILY, GENUS, SPECIES, \nSUBSPECIES, VARIETY, FORM\n"
        examples:
        - value: SPECIES
        - value: SUBSPECIES
        - value: GENUS
          description: When only identified to genus level
      taxonomic_authority:
        required: false
        range: string
        slot_uri: dwc:scientificNameAuthorship
        description: |
          The authorship information for the scientific name.

          **Format**: "Author, Year" or "(Author, Year)" for recombinations          
        examples:
        - value: Linnaeus, 1758
        - value: (Gray, 1821)
          description: Parentheses indicate original genus differs
      higher_classification:
        required: false
        range: string
        slot_uri: dwc:higherClassification
        description: |
          Full taxonomic hierarchy from kingdom to genus.

          **Format**: Pipe-separated: "Kingdom|Phylum|Class|Order|Family|Genus"          
        examples:
        - value: Animalia|Chordata|Aves|Columbiformes|Columbidae|Raphus
          description: Dodo classification
      taxon_remark:
        required: false
        range: string
        slot_uri: dwc:taxonRemarks
        description: |
          Notes about taxonomic identification, uncertainties, or changes.          
        examples:
        - value: Previously classified as Didus ineptus
      identification_qualifier:
        required: false
        range: string
        slot_uri: dwc:identificationQualifier
        description: |
          Qualifier for uncertain identifications.

          **Values**: "cf." (compare with), "aff." (affinity with), "?" (uncertain)          
        examples:
        - value: cf.
          description: Uncertain, compare with named taxon
        - value: aff.
          description: Related to but distinct from named taxon
      identified_by:
        required: false
        range: string
        multivalued: true
        slot_uri: dwc:identifiedBy
        description: |
          Person(s) who made the taxonomic identification.          
        examples:
        - value: Dr. Jane Smith
      date_identified:
        required: false
        range: date
        slot_uri: dwc:dateIdentified
        description: |
          Date when the current identification was made.          
        examples:
        - value: '2020-03-15'
      specimen_type:
        required: false
        range: string
        slot_uri: dwc:typeStatus
        description: "Nomenclatural type status if applicable.\n\n**Values**: HOLOTYPE,\
          \ PARATYPE, SYNTYPE, LECTOTYPE, NEOTYPE, \nTOPOTYPE, ISOTYPE (plants), TYPE\
          \ (informal)\n"
        examples:
        - value: HOLOTYPE
        - value: PARATYPE
      is_type_specimen:
        required: false
        range: boolean
        description: |
          Whether this is a nomenclatural type specimen.
          True if specimen has any type status (holotype, paratype, etc.)          
        examples:
        - value: true
          description: Type specimen
      type_status:
        required: false
        range: string
        slot_uri: dwc:typeStatus
        description: |
          Full type status statement including taxon name.

          **Format**: "Type status of Taxon Name Author, Year"          
        examples:
        - value: Holotype of Raphus cucullatus Linnaeus, 1758
      sex:
        required: false
        range: string
        slot_uri: dwc:sex
        description: |
          Sex of the organism.

          **Values**: MALE, FEMALE, HERMAPHRODITE, UNKNOWN, NOT_APPLICABLE          
        examples:
        - value: MALE
        - value: FEMALE
        - value: UNKNOWN
      life_stage:
        required: false
        range: string
        slot_uri: dwc:lifeStage
        description: |
          Life stage of the organism when collected/preserved.

          **Values vary by taxon**:
          - Vertebrates: ADULT, JUVENILE, SUBADULT, NEONATE
          - Insects: ADULT, LARVA, PUPA, NYMPH, EGG
          - Plants: FLOWERING, FRUITING, VEGETATIVE, SEED          
        examples:
        - value: ADULT
        - value: LARVA
        - value: FLOWERING
      part_type:
        required: false
        range: string
        multivalued: true
        slot_uri: dwc:preparations
        description: "Part(s) of organism represented in this specimen.\n\n**Values**:\
          \ WHOLE_ORGANISM, SKELETON, SKULL, SKIN, SHELL, \nWING, LEG, FEATHER, TISSUE,\
          \ DNA, LEAF, FLOWER, ROOT, SEED\n"
        examples:
        - value: SKELETON
        - value: SKULL
        - value: SKIN
      specimen_count:
        required: false
        range: integer
        slot_uri: dwc:individualCount
        description: |
          Number of individuals represented by this specimen record.
          Default is 1 for most specimens.          
        examples:
        - value: 1
        - value: 50
          description: Lot of 50 insects on one pin/slide
      preservation_method:
        required: false
        range: PreservationMethodEnum
        slot_uri: dwc:preparations
        description: |
          Primary preservation method used for this specimen.

          See PreservationMethodEnum for full list of values.          
        examples:
        - value: TAXIDERMY_MOUNT
        - value: FLUID_ETHANOL
        - value: DRIED_PRESSED
        - value: FROZEN_TISSUE
      preservative_detail:
        required: false
        range: string
        description: |
          Specific details about preservation (concentrations, solutions, etc.).          
        examples:
        - value: 70% ethanol
        - value: Formalin-fixed, ethanol-transferred
        - value: Silica gel dried, stored at -20°C
      preparation_date:
        required: false
        range: date
        description: |
          Date when specimen was prepared/preserved.
          May differ from collection date.          
        examples:
        - value: '2020-06-15'
      prepared_by:
        required: false
        range: string
        slot_uri: crm:P14_carried_out_by
        description: |
          Person or institution who prepared the specimen.          
        examples:
        - value: Natural History Museum Preparation Lab
        - value: J. van der Berg
      collection_date:
        required: false
        range: string
        slot_uri: dwc:eventDate
        description: |
          Date when specimen was collected in the field.

          **Format**: ISO 8601 (YYYY-MM-DD) or range (YYYY-MM-DD/YYYY-MM-DD)
          Can also use text for historical specimens with approximate dates.          
        examples:
        - value: '2020-06-15'
        - value: 2020-06/2020-07
          description: Collected sometime in June-July 2020
        - value: 1870s
          description: Historical specimen with approximate date
      collection_location:
        required: false
        range: CustodianPlace
        inlined: true
        slot_uri: dwc:locality
        description: |
          Structured location where specimen was collected.
          Use for geocoded locations with coordinates.          
        examples:
        - value:
            place_name: Mauritius
            country: MU
            latitude: -20.2
            longitude: 57.5
      collection_locality_text:
        required: false
        range: string
        slot_uri: dwc:verbatimLocality
        description: |
          Verbatim locality description as recorded on label.
          Preserves original text for historical specimens.          
        examples:
        - value: Mauritius, near Port Louis, in forest
        - value: 'Indonesia: Java: Mt. Gede, 1500m'
      collector:
        required: false
        range: string
        multivalued: true
        slot_uri: dwc:recordedBy
        description: |
          Person(s) who collected the specimen.          
        examples:
        - value: Alfred Russel Wallace
        - value: Charles Darwin
      field_number:
        required: false
        range: string
        slot_uri: dwc:fieldNumber
        description: |
          Collector's original field number or catalog number.          
        examples:
        - value: ARW-1234
        - value: CD-HMS Beagle-567
      habitat:
        required: false
        range: string
        slot_uri: dwc:habitat
        description: |
          Description of habitat where specimen was found.          
        examples:
        - value: Tropical rainforest, understory
        - value: Coral reef, depth 15m
      has_associated_taxon:
        required: false
        range: string
        multivalued: true
        slot_uri: dwc:associatedTaxa
        description: |
          Other taxa associated with this specimen (host, parasite, symbiont).

          **Format**: "relationship:Taxon name"          
        examples:
        - value: host:Quercus robur
          description: Insect collected from oak tree
        - value: parasite of:Cervus elaphus
      iucn_status:
        required: false
        range: string
        description: |
          IUCN Red List conservation status.

          **Values**: EX (Extinct), EW (Extinct in Wild), CR (Critically Endangered),
          EN (Endangered), VU (Vulnerable), NT (Near Threatened), LC (Least Concern),
          DD (Data Deficient), NE (Not Evaluated)          
        examples:
        - value: EX
          description: Extinct (e.g., Dodo)
        - value: CR
          description: Critically Endangered
      cites_appendix:
        required: false
        range: string
        description: |
          CITES (Convention on International Trade in Endangered Species) listing.

          **Values**: APPENDIX_I, APPENDIX_II, APPENDIX_III, NOT_LISTED

          Important for legal compliance in specimen transfers.          
        examples:
        - value: APPENDIX_I
          description: Most endangered, trade prohibited
      legal_provenance_note:
        required: false
        range: string
        description: |
          Notes on legal status and provenance for conservation-sensitive specimens.

          Document pre-CITES collection, permits, legal transfers.          
        examples:
        - value: 'Collected pre-CITES (1975). Import permit #12345.'
      gbif_id:
        required: false
        range: string
        slot_uri: dwc:occurrenceID
        description: |
          Global Biodiversity Information Facility occurrence ID.
          Links specimen to GBIF occurrence record.          
        examples:
        - value: https://www.gbif.org/occurrence/1234567890
      bold_id:
        required: false
        range: string
        description: |
          Barcode of Life Data System (BOLD) record ID.
          Links to DNA barcode data.          
        examples:
        - value: BOLD:AAA0001
      genbank_accession:
        required: false
        range: string
        multivalued: true
        description: |
          NCBI GenBank accession numbers for sequences from this specimen.          
        examples:
        - value: MW123456
        - value: MN987654
      has_or_had_custodian_type:
        equals_expression: '["hc:BioCustodianType", "hc:MuseumType", "hc:ResearchOrganizationType"]'
      specificity_annotation:
        range: SpecificityAnnotation
        inlined: true
      template_specificity:
        range: TemplateSpecificityScores
        inlined: true
    comments:
    - BiologicalObject extends ExhibitedObject with biological specimen-specific fields
    - Aligned with Darwin Core (TDWG) vocabulary for biodiversity data
    - Supports natural history museum, botanical garden, and zoo collections
    - Includes taxonomic, preservation, collection event, and conservation data
    - Links to GBIF, BOLD, and GenBank for molecular data integration
    see_also:
    - https://cidoc-crm.org/html/cidoc_crm_v7.1.3.html#E20
    - https://dwc.tdwg.org/terms/
    - https://www.gbif.org/
    - https://www.iucnredlist.org/
    examples:
    - value:
        object_id: https://nde.nl/ontology/hc/object/oum-dodo-head
        object_name: Oxford Dodo
        object_description: "The only surviving dodo soft tissue - a head with preserved\
          \ skin and \nfeathers, plus associated foot. The most complete dodo specimen\
          \ known.\nDonated by Elias Ashmole in 1683.\n"
        taxon_name: Raphus cucullatus (Linnaeus, 1758)
        common_name:
        - Dodo
        - Dronte
        taxonomic_rank: SPECIES
        higher_classification: Animalia|Chordata|Aves|Columbiformes|Columbidae|Raphus
        part_type:
        - HEAD
        - FOOT
        preservation_method: DRIED_WHOLE
        collection_date: pre-1662
        collection_location:
          place_name: Mauritius
          country: MU
        iucn_status: EX
        current_keeper: https://nde.nl/ontology/hc/custodian/uk/oxford-museum-natural-history
        accession_number: OUM 11605
        wikidata_id: Q193493
      description: Oxford Dodo - most complete dodo specimen, Oxford University Museum
    - value:
        object_id: https://nde.nl/ontology/hc/object/naturalis-megatherium
        object_name: Megatherium skeleton
        object_description: |
          Nearly complete skeleton of giant ground sloth from Pleistocene Argentina.
          One of the finest examples of this extinct megafauna.          
        taxon_name: Megatherium americanum Cuvier, 1796
        common_name:
        - Giant Ground Sloth
        taxonomic_rank: SPECIES
        part_type:
        - SKELETON
        preservation_method: FOSSIL_PREPARED
        collection_locality_text: Argentina, Buenos Aires Province
        iucn_status: EX
        current_keeper: https://nde.nl/ontology/hc/custodian/nl/naturalis
      description: Megatherium skeleton at Naturalis Biodiversity Center
    - value:
        object_id: https://nde.nl/ontology/hc/object/kew-type-specimen
        object_name: Quercus robur type specimen
        object_description: |
          Herbarium type specimen of English Oak collected by Linnaeus.          
        taxon_name: Quercus robur L.
        common_name:
        - English Oak
        - Pedunculate Oak
        taxonomic_rank: SPECIES
        taxonomic_authority: Linnaeus, 1753
        specimen_type: LECTOTYPE
        is_type_specimen: true
        type_status: Lectotype of Quercus robur L., designated by Schwarz (1936)
        part_type:
        - LEAF
        - FLOWER
        preservation_method: DRIED_PRESSED
        collection_date: 1750s
        collector:
        - Carl Linnaeus
        current_keeper: https://nde.nl/ontology/hc/custodian/uk/royal-botanic-gardens-kew
      description: Oak type specimen at Royal Botanic Gardens, Kew
slots:
  taxon_name:
    description: Scientific name (Linnean binomial)
    range: string
    slot_uri: dwc:scientificName
  common_name:
    description: Common/vernacular name(s)
    range: string
    multivalued: true
    slot_uri: dwc:vernacularName
  common_name_language:
    description: Language code for common names
    range: string
    multivalued: true
    slot_uri: dcterms:language
  taxonomic_rank:
    description: Taxonomic rank (SPECIES, GENUS, etc.)
    range: string
    slot_uri: dwc:taxonRank
  taxonomic_authority:
    description: Author and year of scientific name
    range: string
    slot_uri: dwc:scientificNameAuthorship
  higher_classification:
    description: Full taxonomic hierarchy
    range: string
    slot_uri: dwc:higherClassification
  taxon_remark:
    description: Notes about taxonomic identification
    range: string
    slot_uri: dwc:taxonRemarks
  identification_qualifier:
    description: Qualifier for uncertain identifications (cf., aff.)
    range: string
    slot_uri: dwc:identificationQualifier
  identified_by:
    description: Person who made the identification
    range: string
    multivalued: true
    slot_uri: dwc:identifiedBy
  date_identified:
    description: Date of current identification
    range: date
    slot_uri: dwc:dateIdentified
  specimen_type:
    description: Nomenclatural type status
    range: string
    slot_uri: dwc:typeStatus
  is_type_specimen:
    description: Whether this is a type specimen
    range: boolean
  type_status:
    description: Full type status statement
    range: string
    slot_uri: dwc:typeStatus
  sex:
    description: Sex of organism
    range: string
    slot_uri: dwc:sex
  life_stage:
    description: Life stage when collected
    range: string
    slot_uri: dwc:lifeStage
  part_type:
    description: Part(s) of organism represented
    range: string
    multivalued: true
    slot_uri: dwc:preparations
  specimen_count:
    description: Number of individuals in specimen
    range: integer
    slot_uri: dwc:individualCount
  preservation_method:
    description: Primary preservation method
    range: PreservationMethodEnum
    slot_uri: dwc:preparations
  preservative_detail:
    description: Specific preservation details
    range: string
  preparation_date:
    description: Date specimen was prepared
    range: date
  prepared_by:
    description: Person/institution that prepared specimen
    range: string
    slot_uri: crm:P14_carried_out_by
  collection_date:
    description: Date specimen was collected
    range: string
    slot_uri: dwc:eventDate
  collection_location:
    description: Structured collection location
    range: CustodianPlace
    slot_uri: dwc:locality
  collection_locality_text:
    description: Verbatim locality description
    range: string
    slot_uri: dwc:verbatimLocality
  collector:
    description: Person(s) who collected specimen
    range: string
    multivalued: true
    slot_uri: dwc:recordedBy
  field_number:
    description: Collector's field number
    range: string
    slot_uri: dwc:fieldNumber
  habitat:
    description: Habitat description
    range: string
    slot_uri: dwc:habitat
  has_associated_taxon:
    description: Associated taxa (host, parasite, etc.)
    range: string
    multivalued: true
    slot_uri: dwc:associatedTaxa
  iucn_status:
    description: IUCN Red List status
    range: string
  cites_appendix:
    description: CITES appendix listing
    range: string
  legal_provenance_note:
    description: Notes on legal status for CITES species
    range: string
  gbif_id:
    description: GBIF occurrence ID
    range: string
    slot_uri: dwc:occurrenceID
  bold_id:
    description: BOLD barcode record ID
    range: string
  genbank_accession:
    description: GenBank accession numbers
    range: string
    multivalued: true